Sulfide exposure results in enhanced sqr transcription through upregulating the expression and activation of HSF1 in echiuran worm Urechis unicinctus

Toxic effect of chromium on nonspecific immune, bioaccumulation, and tissue structure of Urechis unicinctus

The contamination of toxic heavy metals in aquatic environments has garnered significant global attention due to its detrimental effects on marine organisms and human health. Hexavalent chromium is a typical environmental and occupational heavy metal pollutant, identified as carcinogenic heavy metal. This study aimed to assess the impact of different Cr (VI) concentrations (0.05-2.5 mg/L) on Urechis unicinctus (U. unicinctus) by investigating bioaccumulation, antioxidant defense system, expression of resistance-related genes, and histological issues. A clear concentration-effect relationship was observed in the bioaccumulation of Cr (VI) in muscle tissues of U. unicinctus. Moreover, exposure to Cr (VI) can alter the activities of lysozyme (LSZ), catalase (CAT), and superoxide dismutase (SOD) to enhance cellular defense mechanisms in U. unicinctus. Likewise, maintained the normal protein structure and functional stability by regulating protein folding. The heat shock cognitive protein (HSC70) gene showed an upward and then downward trend after Cr (VI) exposure. At 12 h, the HSC70 gene expression reached the maximum values of 4.75 and 4.61-fold in the 0.1 and 1.5 mg/L groups, respectively. The organism produced a large number of free radicals, and elevated level of metallothionein (MT) was used to scavenge free radicals and alleviate oxidative stress. Additionally, histopathological examination revealed disorganization in the midgut, atrophic changes in intestinal connective tissue, uneven distribution in respiratory tissues, and irregular shape with a significant reduction in epithelial cells within the gastric cavity. These findings can serve as a valuable reference for elucidating the toxicity mechanisms of heavy metals towards marine benthic organisms and enhancing water environment monitoring strategies.

Genome-wide identification and expression analyses of Toll-like receptors provide new insights on adaptation to intertidal benthic environments in Urechis unicinctus (Annelida, Echiura)

Toll-like receptors (TLR) are an important class of pattern recognition receptors involved in innate immunity that recognize pathogen-associated and damage-associated molecular patterns. Although the role of TLRs in immunity has been extensively studied, a systematic investigation of their function in environmental adaptation is still in its infancy. In this study, a genome-wide search was conducted to systematically investigate TLR family members of Urechis unicinctus, a typical benthic organism in intertidal mudflats. A total of 28 TLR genes were identified in the U. unicinctus genome, and their fundamental physiological and biochemical properties were characterized. Gene copy number analysis among species in different habitats indicated that TLR family gene expansion may be probably related with benthic environmental adaptation. To further investigate the expression patterns of TLR members under environmental stress, transcriptome data was analyzed from different developmental stages and the hindgut under sulfide stress. Transcriptome analysis of different developmental stages showed that most TLR genes were highly expressed during a key period of benthic environment adaptation (worm-shaped larva). Transcriptome analysis of the hindgut under sulfide stress showed that the expression of 12 TLR members was significantly induced under sulfide stress. These results indicate that the regulation of TLR gene expression may be probably involved in the adaptation of U. unicinctus to the benthic intertidal zone environment. Taken together, this study may lay the foundation for future functional analysis of the specific role of TLRs in host immune responses against sulfide exposure and benthic environmental stress in annelid.

Identification and validation of the reference genes in the echiuran worm Urechis unicinctus based on transcriptome data

BACKGROUND

Real-time quantitative PCR (RT-qPCR) is a crucial and widely used method for gene expression analysis. Selecting suitable reference genes is extremely important for the accuracy of RT-qPCR results. Commonly used reference genes are not always stable in various organisms or under different environmental conditions. With the increasing application of high-throughput sequencing, transcriptome analysis has become an effective method for identifying novel stable reference genes.

RESULTS

In this study, we identified candidate reference genes based on transcriptome data covering embryos and larvae of early development, normal adult tissues, and the hindgut under sulfide stress using the coefficient of variation (CV) method in the echiuran Urechis unicinctus, resulting in 6834 (15.82%), 7110 (16.85%) and 13880 (35.87%) candidate reference genes, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the candidate reference genes were significantly enriched in cellular metabolic process, protein metabolic process and ribosome in early development and normal adult tissues as well as in cellular localization and endocytosis in the hindgut under sulfide stress. Subsequently, ten genes including five new candidate reference genes and five commonly used reference genes, were validated by RT-qPCR. The expression stability of the ten genes was analyzed using four methods (geNorm, NormFinder, BestKeeper, and ∆Ct). The comprehensive results indicated that the new candidate reference genes were more stable than most commonly used reference genes. The commonly used ACTB was the most unstable gene. The candidate reference genes STX12, EHMT1, and LYAG were the most stable genes in early development, normal adult tissues, and hindgut under sulfide stress, respectively. The log₂(TPM) of the transcriptome data was significantly negatively correlated with the Ct values of RT-qPCR (Ct =  - 0.5405 log₂(TPM) + 34.51), which made it possible to estimate the Ct value before RT-qPCR using transcriptome data.

CONCLUSION

Our study is the first to select reference genes for RT-qPCR from transcriptome data in Echiura and provides important information for future gene expression studies in U. unicinctus.

Genome-Wide Analyses of Heat Shock Protein Superfamily Provide New Insights on Adaptation to Sulfide-Rich Environments in Urechis unicinctus (Annelida, Echiura)

The intertidal zone is a transitional area of the land-sea continuum, in which physical and chemical properties vary during the tidal cycle and highly toxic sulfides are rich in sediments due to the dynamic regimes. As a typical species thriving in this habitat, Urechis unicinctus presents strong sulfide tolerance and is expected to be a model species for sulfide stress research. Heat shock proteins (HSPs) consist of a large group of highly conserved molecular chaperones, which play important roles in stress responses. In this study, we systematically analyzed the composition and expression of HSPs in U. unicinctus. A total of eighty-six HSP genes from seven families were identified, in which two families, including sHSP and HSP70, showed moderate expansion, and this variation may be related to the benthic habitat of the intertidal zone. Furthermore, expression analysis revealed that almost all the HSP genes in U. unicinctus were significantly induced under sulfide stress, suggesting that they may be involved in sulfide stress response. Weighted gene co-expression network analysis (WGCNA) showed that 12 HSPs, including 5 sHSP and 4 HSP70 family genes, were highly correlated with the sulfide stress response which was distributed in steelblue and green modules. Our data indicate that HSPs, especially sHSP and HSP70 families, may play significant roles in response to sulfide stress in U. unicinctus. This systematic analysis provides valuable information for further understanding of the function of the HSP gene family for sulfide adaptation in U. unicinctus and contributes a better understanding of the species adaptation strategies of marine benthos in the intertidal zone.

Screening and Identification of Transcription Factors Potentially Regulating Foxl2 Expression in Chlamys farreri Ovary

Foxl2 is an evolutionarily conserved female sex gene, which is specifically expressed in the ovary and mainly involved in oogenesis and ovarian function maintenance. However, little is known about the mechanism that regulates Foxl2 specific expression during the ovary development. In the present study, we constructed the gonadal yeast one-hybrid (Y1H) library of Chlamysfarreri with ovaries and testes at different developmental stages using the Gateway technology. The library capacity was more than 1.36 × 10⁷ CFU, and the length of the inserted fragment was 0.75 Kb~2 Kb, which fully met the demand of yeast library screening. The highly transcriptional activity promoter sequence of C. farreri Foxl2 (Cf-Foxl2) was determined at -1000~-616 bp by dual-luciferase reporter (DLR) assay and was used as bait to screen possible transcription factors from the Y1H library. Eleven candidate factors, including five unannotated factors, were selected based on Y1H as well as their expressional differences between ovaries and testes and were verified for the first time to be involved in the transcriptional regulation of Cf-Foxl2 by RT-qPCR and DLR. Our findings provided valuable data for further studying the specific regulation mechanism of Foxl2 in the ovary.

A novel transcription factor MRPS27 up-regulates the expression of sqr, a key gene of mitochondrial sulfide metabolism in echiuran worm Urechis unicinctus

Hydrogen sulfide is a natural, widely distributed, poisonous substance and sulfide: quinone oxidoreductase (SQR) is responsible for oxidizing hydrogen sulfide to less toxic sulfur compounds. The increase of SQR mRNA level is an important mechanism for organisms to adapt to hydrogen sulfide-rich environments. However, its transcriptional regulation mechanism is not very clear. In this study, a mitochondrial 28S ribosomal protein S27 (MRPS27), which has never been reported as a transcription factor, was screened by yeast one-hybrid experiment from the echiuran worm Urechis unicinctus, a benthic organism living in marine sediments. Western blotting indicated that UuMRPS27 contents increased significantly in the nuclear extract of hindgut under exposed to 150 μM sulfide. ChIP and EMSA assays demonstrated that UuMRPS27 did bind to the sqr proximal promoter, the key binding sequence was CTAGAG (+12 to +17 of the promoter) detected by DNase I footprinting assay as well as transient transfection experiments. Furthermore, UuMRPS27, as a transcription activator, exhibited the highest transcription activity compared with other reported sqr transcription factors. Our data revealed for the first time the role of MRPS27 acting as a transcription factor which expanded the understanding of sqr transcriptional regulation in sulfide metabolism mechanism.

A novel transcription factor Rwdd1 and its SUMOylation inhibit the expression of sqr, a key gene of mitochondrial sulfide metabolism in Urechis unicinctus

Sulfide-quinone oxidoreductase (SQR) is a key enzyme of sulfide metabolism in metazoans, and responsible for oxidizing sulfide into thiosulfate and transmitting the generated electrons to the ubiquinone. It has been revealed that the sqr mRNA level increases significantly in echiuran worm Urechis unicinctus exposed to sulfide, and HSF1, NF1 and Sp1 have been verified to participate in its transcriptional regulation. In this study, we obtained 23 potential transcription factors interacting possibly with the proximal region (-391 to +50) of sqr promoter, and focused on the RWD domain-containing 1 (Rwdd1), a protein with the maximum number of clones in yeast one-hybrid (Y1H) screening, to investigate its transcriptional regulation to U. unincitus sqr. The ChIP and EMSA assays identified that the Rwdd1 can bind directly to the promoter (+18/+36) of U. unicinctus sqr. The point mutation and transient transfection experiments discovered that TACG was the key sequence of the DNA element bound by the Rwdd1. Furthermore, the U. unicinctus Rwdd1 (UuRwdd1) was identified to be a transcription repressor inhibiting the sqr promoter activity, and the SUMOylation of UuRwdd1 at the lysine of 90^th enhanced its inhibitory effect on sqr transcription further. Western blotting found Rwdd1 responded to sulfide in hindguts from U. unincitus, and the protein content showed a remarkable drop in hindgut nuclei in the early sulfide exposure, and then increased significantly both in the total protein and the nuclear protein extract. We suggested that the Rwdd1 is a novel transcription factor, and these data improve our understanding of the sqr transcriptional regulation and the mitochondrial sulfide metabolism.

Molecular evolution and expression of oxygen transport genes in livebearing fishes (Poeciliidae) from hydrogen sulfide rich springs

Hydrogen sulfide (H2S) is a natural toxicant in some aquatic environments that has diverse molecular targets. It binds to oxygen transport proteins, rendering them non-functional by reducing oxygen-binding affinity. Hence, organisms permanently inhabiting H2S-rich environments are predicted to exhibit adaptive modifications to compensate for the reduced capacity to transport oxygen. We investigated 10 lineages of fish of the family Poeciliidae that have colonized freshwater springs rich in H2S—along with related lineages from non-sulfidic environments—to test hypotheses about the expression and evolution of oxygen transport genes in a phylogenetic context. We predicted shifts in the expression of and signatures of positive selection on oxygen transport genes upon colonization of H2S-rich habitats. Our analyses indicated significant shifts in gene expression for multiple hemoglobin genes in lineages that have colonized H2S-rich environments, and three hemoglobin genes exhibited relaxed selection in sulfidic compared to non-sulfidic lineages. However, neither changes in gene expression nor signatures of selection were consistent among all lineages in H2S-rich environments. Oxygen transport genes may consequently be predictable targets of selection during adaptation to sulfidic environments, but changes in gene expression and molecular evolution of oxygen transport genes in H2S-rich environments are not necessarily repeatable across replicated lineages.

The roles of plasticity and evolutionary change in shaping gene expression variation in natural populations of extremophile fish

The notorious plasticity of gene expression responses and the complexity of environmental gradients complicate the identification of adaptive differences in gene regulation among populations. We combined transcriptome analyses in nature with common-garden and exposure experiments to establish cause-effect relationships between the presence of a physiochemical stressor and expression differences, as well as to test how evolutionary change and plasticity interact to shape gene expression variation in natural systems. We studied two evolutionarily independent population pairs of an extremophile fish (Poecilia mexicana) living in toxic, hydrogen sulphide (H₂ S)-rich springs and adjacent nontoxic habitats and assessed genomewide expression patterns of wild-caught and common-garden-raised individuals exposed to different concentrations of H₂ S. We found that 7.7% of genes that were differentially expressed between sulphidic and nonsulphidic ecotypes remained differentially expressed in the laboratory, indicating that sources of selection other than H₂ S-or plastic responses to other environmental factors-contribute substantially to gene expression patterns observed in the wild. Concordantly differentially expressed genes in the wild and the laboratory were primarily associated with H₂ S detoxification, sulphur processing and metabolic physiology. While shared, ancestral plasticity played a minor role in shaping gene expression variation observed in nature, we documented evidence for evolved population differences in the constitutive expression as well as the H₂ S inducibility of candidate genes. Mechanisms underlying gene expression variation also varied substantially across the two ecotype pairs. These results provide a springboard for studying evolutionary modifications of gene regulatory mechanisms that underlie expression variation in locally adapted populations.

Complexities of gene expression patterns in natural populations of an extremophile fish (Poecilia mexicana, Poeciliidae)

Variation in gene expression can provide insights into organismal responses to environmental stress and physiological mechanisms mediating adaptation to habitats with contrasting environmental conditions. We performed an RNA-sequencing experiment to quantify gene expression patterns in fish adapted to habitats with different combinations of environmental stressors, including the presence of toxic hydrogen sulphide (H2 S) and the absence of light in caves. We specifically asked how gene expression varies among populations living in different habitats, whether population differences were consistent among organs, and whether there is evidence for shared expression responses in populations exposed to the same stressors. We analysed organ-specific transcriptome-wide data from four ecotypes of Poecilia mexicana (nonsulphidic surface, sulphidic surface, nonsulphidic cave and sulphidic cave). The majority of variation in gene expression was correlated with organ type, and the presence of specific environmental stressors elicited unique expression differences among organs. Shared patterns of gene expression between populations exposed to the same environmental stressors increased with levels of organismal organization (from transcript to gene to physiological pathway). In addition, shared patterns of gene expression were more common between populations from sulphidic than populations from cave habitats, potentially indicating that physiochemical stressors with clear biochemical consequences can constrain the diversity of adaptive solutions that mitigate their adverse effects. Overall, our analyses provided insights into transcriptional variation in a unique system, in which adaptation to H2 S and darkness coincide. Functional annotations of differentially expressed genes provide a springboard for investigating physiological mechanisms putatively underlying adaptation to extreme environments.

Response of gut health and microbiota to sulfide exposure in Pacific white shrimp Litopenaeus vannamei

Sulfide is a natural and widely distributed toxicant. It can be commonly found on the interface between water and sediment in the aquatic environment. The Pacific white shrimp Litopenaeus vannamei starts life in the benthic zone soon after the mysis stage, an early stage of post larvae. Therefore, L. vannamei is inevitably affected by exposure to sulfide released from pond sediment. This study explored the toxicant effect of different concentrations of sulfide on the intestinal health and microbiota of Pacific white shrimp by monitoring the change of expression of inflammatory, immune related cytokines, and the structure of the intestinal microbiota. The gut histology, expressions of inflammatory and immune related cytokines (tumor necrosis factor-alpha, C-type lectin 3, myostatin and heat shock transcription factor 1), and the microbiota were determined in L. vannamei after exposure to 0 (control), 425.5 (1/10 LC 50-96 h), and 851 μg/L (1/5 LC 50-96 h) of sulfide for 21 days. With the increase of sulfide concentration, intestinal injury was aggravated and the inflammatory and immune related cytokines generated a range of reactions. The expression of myostatin (MSTN) was significantly down-regulated by the concentration of sulfide exposure. No difference in the expression of heat shock transcription factor 1 (HSF1) was found between the control and shrimp exposed to 425.5 μg/L, but significantly higher HSF1 expression was found in shrimp exposed to 851 μg/L of sulfide. Significantly higher values of tumor necrosis factor-alpha (TNF-α) and C-type lectin 3 (CTL3) were found in the shrimp exposed to 425.5 μg/L of sulfide compared to the control, but a lower value was found in the shrimp exposed to 851 μg/L (P < 0.05). Sulfide also changed the intestinal microbial communities. The abundance of pathogenic bacteria, such as Cyanobacteria, Vibrio and Photobacterium, increased significantly with exposure to the increasing concentration of sulfide. The abundance of some anti-stress bacteria, such as Chlorobi and Fusobacterium, increased. Nitrospirae which can alleviate nitrite toxicity decreased. Microbacterium, Parachlamydia, and Shewanella were all commonly found and down-regulated in both sulfide groups, which is associated with an adaptation to sulfide stimulation. This study indicates that chronic exposure to sub-lethal levels of sulfide could lead to damage of the gut structure, stimulate the response of the inflammatory and immune systems, and shape the structure of the gut microbiota in L. vannamei.

NF1, Sp1 and HSF1 are synergistically involved in sulfide-induced sqr activation in echiuran worm Urechis unicinctus

BACKGROUND

Sulfide is a well-known environmental toxic substance. Mitochondrial sulfide oxidation is a main mechanism of sulfide detoxification in organisms, and sulfide: quinone oxidoreductase (SQR) is a key enzyme which is involved in transferring electrons from sulfide to ubiquinone and converting sulfide into thiosulfate. Previous studies have revealed the SQR-mediated mitochondrial sulfide oxidation exists in the echiuran worm Urechis unicinctus, and its sqr mRNA level increased significantly when the worm is exposed to sulfide. In this study, we attempt to reveal the synergistic regulation of transcription factors on sulfide-induced sqr transcription in U. unicinctus.

METHODS

ChIP and EMSA were used to identify the interactions between sqr proximal promoter (from -391 to +194bp) and transcription factors NF1 (nuclear factor 1) and Sp1 (specificity protein 1). Site-directed mutation and transfection assays further revealed their binding sites and synergistic roles of HSF1, NF1 and Sp1 in the sqr transcription. When U. unicinctus were exposed to 150μM sulfide, the expression levels and nuclear contents of NF1 and Sp1 were examined by Western blotting, and the binding contents between NF1 or Sp1 and the sqr promoter were also detected by ChIP.

RESULTS

Transcription factors NF1 and Sp1 were confirmed to interact with the sqr proximal promoter, and their binding sites were identified in -75 to -69bp for NF1 and -210 to -201bp for Sp1. Transfection assays showed mutation of NF1 or Sp1 binding site significantly decreased the sqr promoter activity by 50% or 73%, respectively. Moreover, we demonstrated three transcription factors NF1, Sp1 and HSF1 enhanced synergistically the activity of sqr transcription. Furthermore, contents of NF1 or Sp1 binding to the sqr proximal region increased significantly in the hindgut when the worms were exposed to 150μM sulfide. Similar changes of NF1 or Sp1 levels and nuclear NF1 or Sp1 levels were also presented.

CONCLUSION

Transcription factors NF1, Sp1 and HSF1 are all involved in sulfide-induced sqr transcription. Sulfide can activate sqr transcription by not only increasing their expression levels, but also promoting them entering nucleus and binding to the sqr promoter. NF1 and Sp1 participate in both basal and sulfide-induced sqr transcription, while HSF1 functions mainly in sulfide-induced sqr transcription.

Mechanisms Underlying Adaptation to Life in Hydrogen Sulfide-Rich Environments

Hydrogen sulfide (H2S) is a potent toxicant interfering with oxidative phosphorylation in mitochondria and creating extreme environmental conditions in aquatic ecosystems. The mechanistic basis of adaptation to perpetual exposure to H2S remains poorly understood. We investigated evolutionarily independent lineages of livebearing fishes that have colonized and adapted to springs rich in H2S and compared their genome-wide gene expression patterns with closely related lineages from adjacent, nonsulfidic streams. Significant differences in gene expression were uncovered between all sulfidic and nonsulfidic population pairs. Variation in the number of differentially expressed genes among population pairs corresponded to differences in divergence times and rates of gene flow, which is consistent with neutral drift driving a substantial portion of gene expression variation among populations. Accordingly, there was little evidence for convergent evolution shaping large-scale gene expression patterns among independent sulfide spring populations. Nonetheless, we identified a small number of genes that was consistently differentially expressed in the same direction in all sulfidic and nonsulfidic population pairs. Functional annotation of shared differentially expressed genes indicated upregulation of genes associated with enzymatic H2S detoxification and transport of oxidized sulfur species, oxidative phosphorylation, energy metabolism, and pathways involved in responses to oxidative stress. Overall, our results suggest that modification of processes associated with H2S detoxification and toxicity likely complement each other to mediate elevated H2S tolerance in sulfide spring fishes. Our analyses allow for the development of novel hypotheses about biochemical and physiological mechanisms of adaptation to extreme environments.